Epidemic Network

Experimental environment for testing of large array of theoretical conditions for development epidemic event within various quantitative, spatial and connectedness (network structure) aspects.

Inputs

Name	Type	Description
seed	integer	random generator seed number used as `random-seed seed`.
initial-households	integer	initial count of households.
population-coefficient	integer	household size variance coefficient (mean of exponential distribution).
initial-clusters	integer	initial count of clusters/settlements.
cluster-radius-min, cluster-radius-max	integer	minimum/maximum cluster radius used to sample a random cluster radius from an uniform distribution, as `in-radius (min-cluster-radius + (random max-cluster-radius))`.
search-radius	integer	maximum search distance to establish links.
max-connections	integer	maximum number of connections (links) per distance range.
initial-infected	integer	number of initial cases or people agents initialised with the "incubation" stage and a stochastic state of stage 1 counter.
max-daily-contacts	integer	maximum number of connections to be considered contacts each day.
duration-latent-mean, duration-latent-stddev	float	Mean and standard deviation of duration of the latent stage of the disease, used in `random-normal duration-latent-mean duration-latent-stddev`.
duration-prodromal-mean, duration-prodromal-stddev	float	Mean and standard deviation of duration of the prodromal stage of the disease, used in `random-normal duration-prodromal-mean duration-prodromal-stddev`.
duration-contagious-mean, duration-contagious-stddev	float	Mean and standard deviation of duration of the contagious stage of the disease, used in `random-normal duration-contagious-mean duration-contagious-stddev`.
mortality-rate	float	Average mortality rate applied to all individuals (`people`) in the population.
transmission-prob-range1-mean, transmission-prob-range1-stddev	float	Mean and standard deviation of transmission probability towards people within range 1 (search-radius * 0.125), used in `random-normal transmission-prob-range1-mean transmission-prob-range1-stddev`.
transmission-prob-range2-mean, transmission-prob-range2-stddev	float	Mean and standard deviation of transmission probability towards people within range 2 (search-radius * 0.25), used in `random-normal transmission-prob-range2-mean transmission-prob-range2-stddev`.
transmission-prob-range3-mean, transmission-prob-range3-stddev	float	Mean and standard deviation of transmission probability towards people within range 3 (search-radius * 0.5), used in `random-normal transmission-prob-range3-mean transmission-prob-range3-stddev`.
transmission-prob-range4-mean, transmission-prob-range4-stddev	float	Mean and standard deviation of transmission probability towards people within range 4 (search-radius), used in `random-normal transmission-prob-range4-mean transmission-prob-range4-stddev`.
range1-search-radius-share, range2-search-radius-share, range3-search-radius-share, range4-search-radius-share	float	the proportion of `search-radius` effective for each transmission range.
range1-initial-connections-share, range2-initial-connections-share, range3-initial-connections-share, range4-initial-connections-share	float	the proportion of `max-connections` from which a random sample is taken as initial contacts of the infected people for each distance range.

Outputs

Name	Type	Description
pos-spread	integer	Count of positive disease transmission encounter of an individual (passed to other person)
neg-spread	integer	Count of negative disease transmission encounter of an individual (not passed to other person)
count-spread	integer	Cumulative number of daily contacts
count-daily-contact	integer	Sum of all daily contacts for the actual day (reset each day)
count-daily-transmission	integer	Sum of all daily disease transmission encounter for the actual day (reset each day)
count-daily-transmission-pers	integer	Number of people with the potential to performing a disease transmission encounter for the actual day (reset each day)
nw-betcen	float	Network metrics':' betweenness centrality
nw-eigcen	float	Network metrics':' eigenvector centrality
nw-clocen	float	Network metrics':' closeness centrality
nw-clucoe	float	Network metrics':' clustering coefficient
nw-mod	float	Network metrics':' modularity

Epidemic Network

What Epidemic Network can do for you

Inputs

Outputs

Mentions

Contributors

Member of community